Oldest Hominine DNA Sequenced

Mitochondrial genome of a 400,000-year-old representative of the genus Homo sequenced

Thursday, 05 December 2013

This is a skeleton of a Homo heidelbergensis 

from Sima de los Huesos, a unique cave site in

Northern Spain. Credit: Javier Trueba, Madrid 
Scientific Films. 

Using novel techniques to extract and study ancient DNA researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have determined an almost complete mitochondrial genome sequence of a 400,000-year-old representative of the genus Homo from Sima de los Huesos, a unique cave site in Northern Spain, and found that it is related to the mitochondrial genome of Denisovans, extinct relatives of Neanderthals in Asia. DNA this old has until recently been retrieved only from the permafrost.

Sima de los Huesos (SH), the "bone pit", is a cave site in Northern Spain that has yielded the world's largest assembly of Middle Pleistocene hominine fossils, consisting of at least 28 skeletons, which have been excavated and pieced together over the course of more than two decades by a Spanish team of palaeontologists led by Juan-Luis Arsuaga. The fossils are classified as Homo heidelbergensis but also carry traits typical of Neanderthals. Until now it had not been possible to study the DNA of these unique hominines.

Matthias Meyer at work in the clean lab. 
Credit: Max Planck Institute for 
Evolutionary Anthropology. 

Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominine thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neanderthals, Denisovans, present-day humans, and apes.

The Sima de los Huesos hominines lived

approximately 400,000 years ago during the

Middle Pleistocene. Credit: Javier Trueba, 
Madrid Scientific Films.

From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominine lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neanderthals, about 700,000 years ago.

"The fact that the mtDNA of the Sima de los Huesos hominine shares a common ancestor with Denisovan rather than Neanderthal mtDNAs is unexpected since its skeletal remains carry Neanderthal-derived features", says Matthias Meyer.

Considering their age and Neanderthal-like features, the Sima hominines were likely related to the population ancestral to both Neanderthals and Denisovans. Another possibility is that gene flow from yet another group of hominines brought the Denisova-like mtDNA into the Sima hominines or their ancestors.

"Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old. This opens prospects to study the genes of the ancestors of Neanderthals and Denisovans. It is tremendously exciting" says Svante Pääbo, director at the Max Planck Institute for Evolutionary Anthropology.

Prof. Juan Luis Arsuaga, Director of the Centro

Mixto de Evolución and Compòrtamiento

Humanos in Madrid, Spain. Credit: Javier 
Trueba, Madrid Scientific Films. 

"This unexpected result points to a complex pattern of evolution in the origin of Neanderthals and modern humans. I hope that more research will help clarify the genetic relationships of the hominines from Sima de los Huesos to Neanderthals and Denisovans" says Juan-Luis Arsuaga, director of the Center for Research on Human Evolution and Behaviour. The researchers are now pursuing this goal by focusing on retrieving DNA from more individuals from this site and on retrieving also nuclear DNA sequences.

Source: Max-Planck-Gesellschaft 

Contact: Dr. Matthias Meyer

Reference:

A mitochondrial genome sequence of a hominine from Sima de los Huesos

Matthias Meyer, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell and Svante Pääbo

Nature, 4 December 2013, DOI: 10.1038/nature12788

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